Galaxy interactive environments

Anton Kovalsky
  • Updated

Using Galaxy with Terra

Galaxy is an open web-based platform for highly accessible bioinformatic research, similar to Terra. You can learn. more about how to use Galaxy in the platform's documentation or by visiting the Galaxy community hub

Navigating Galaxy's Interface

After clicking "Launch Galaxy" you'll be taken to the main screen of your new Galaxy instance. The Galaxy interface has three panels:Screen_Shot_2021-06-09_at_2.01.41_PM.png

  • The left panel is the Tool panel, where you can see a list of all of the tools that have been pre-installed on this Galaxy instance.
  • The middle panel is for running tools and examining data.
  • The right panel is the History panel, which serves as a convenient place to track your analysis and perform certain actions.

Launching a Galaxy instance

  1. Start by entering a workspace for which you have the permission necessary to launch a notebook VM, and navigate to the Notebooks tab of that workspace. There, you'll click a button labeled "Create a Cloud Environment for Galaxy"

    2021-06-09_12-45-14.png
  2. This will call up the following panel on the right of your screen. This is where you can customize the compute power of your virtual machine and size of the associated disk. Note that the cost of running this environment is higher than for the default notebook configuration, so make sure you use your time wisely!
                               
                                                image.png
  3. Click "Next" and confirm on the screen that follows. Once you've done that, you'll see at the top of your screen a notification that says your Galaxy environment is being provisioned (this can take about 10 minutes):
                              
                                                image__1_.png
  4. When this process is complete, you'll see the following pop-up. Clicking "Launch Galaxy" will take you directly to your very own Galaxy instance

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Note that you'll see the “Cloud compute profile” dialog box both when you first create your Galaxy app instance, then again after the Galaxy app has been created in case you'd like to view what configs you chose. It's important to note two things about this dialog:

  • The purpose of its appearance after the app has already been created is both to show you the current configuration, and to enable you to see a cost estimate for either that configuration or another hypothetical configuration you're thinking of using instead.
  • Terra does not currently support the ability to update the compute configuration of a Galaxy application that is already running, so if you decide you want to change an existing configuration, you'll need to delete that instance and recreate it with a different configuration.

Cloud Environment Persistence

Terra's Galaxy Cloud Environment instances come with a persistent disk in the same way as our Jupyter Notebooks. The persistent disk is a form of storage that retains certain package configurations and outputs so that you don't lose this data in the event that you have to delete and re-create your Galaxy instance. 

This means that when you create a Galaxy instance and then later delete that instance, you will have the option to either keep or delete this persistent disk. After clicking "Delete Environment Options", you'll see your options for what should happen to the persistent disk. If you choose to keep the disk, the next time you create a Galaxy instance the old disk is automatically attached to the new Galaxy instance when you click "Create".

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To learn more about how persistent disks function in all of our cloud environments check out our article on detachable persistent disks here . Two notable differences between Galaxy persistent disks and those for non-Galaxy cloud environments are:

  • Since you can't access a terminal view through our Galaxy instance, the mounted directory is not visible to you through command line tools.
  • Since we don't currently support updating a Galaxy persistent disk once it's created, the option to change the disk size upon Galaxy creation will be disabled if you already have a persistent disk.

Pausing/Resuming a Galaxy instance

When you're using a Galaxy instance, remember that you're being charged on an hourly basis the whole time that the app is running, even if you're not actively using it. For this reason, you may sometimes wish to pause the cloud environment in order to avoid incurring unnecessary costs. To pause and resume your Galaxy instance, follow these steps:

Pause

To pause your Galaxy app, click the Galaxy widget button to the left of the Cloud Environment widget button at the top right of your screen when you are in your workspace:

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This will call up the window below, where you can click "Pause" at the bottom: 

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After a few minutes, the Galaxy widget button will now say "Paused", and you won't be incurring any charges until you resume running the Galaxy instance:

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Resume

To resume your Galaxy app, you can click on the Galaxy widget when it says "Paused". You will then see the box shown below, where you can click "Resume":

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The text in the Galaxy widget button will then change from "Paused" to "Prestarting", then to "Resuming", and eventually back to "Running":

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Once the widget says "Running" again, you will also see the pop-up box prompting you to launch Galaxy:

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If you close that pop-up without launching the Galaxy app, you can still click on the Galaxy button when it says "Running" to call up the Galaxy widget, and click "Launch Galaxy" from there as well.

You can learn more of the details about how pausing and resuming Terra cloud environments in this article on Terra's Jupyter Notebooks environments. Please keep in mind the following key differences between Jupyter and Galaxy instances on Terra:

  • As opposed to Jupyter notebooks, Terra doesn't support auto-pause for Galaxy at this time.
  • As opposed to Jupyter notebooks, a paused Galaxy instance has to be resumed before it can be deleted.

How to import data to your Galaxy instance through the Tool panel

  1. To add data to your Galaxy instance, you'll want to click the upload icon at the top of the Tool panel.

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  2. This will call a pop up that allows you to either upload files from a local machine or to link to other data. Clicking "Choose remote files" will allow you to select the files from your Terra workspace.
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  3. Once you've selected your desired files, the "Start" button, and the files you've selected will appear in the History panel. Once an upload is complete, the item in the History panel turns green.

    Screen_Shot_2020-10-21_at_6.20.57_PM.png
  4. You'll be able to manipulate the files in your history to use them as workflow inputs or data visualization outputs. Once the files are uploaded, you can use, copy, share, or extract them:

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Note that when selecting files, Galaxy will need to be told what format to expect for each of those files. Galaxy does have auto-detecting capabilities, but sometimes it's better to select the filetype yourself:

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How to install additional tools in the Galaxy Tool panel

If your Tool panel is missing something you need for your analysis, you can add tools from thousands repositories available to you.
  1. To add a tool to your Tool panel, start by clicking "Admin" in the masthead at the top of your screen:

    2020-10-21_2226.png
  2. Now, you'll see a menu on the left side of your screen that includes a "Tool Management" section near the bottom. Click the "Install and Uninstall" option in that section:

    2020-10-21_2228.png
  3. This will allow you to search thousands of repositories for the tools that best suit your workflow. The search results give some useful information to help you make the best selection:
    1. How up-to-date is this tool? (Updated date)
    2. How popular is this tool? (Number of downloads)
    3. Who published this tool? (Please note: "IUC" stands for Intergalactic Utilities Commission - a Galaxy community effort to publish best practices)

      Screen_Shot_2020-10-21_at_10.32.01_PM.png
  4. Click "Ok" to install and choose the section in your Tool panel where you'd like the new tool to appear:

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How to create a new history in Galaxy

  1. Select the “multiple histories” button at the top right of the Galaxy history panel.
  2. On the new page, choose “Create new”.
  3. Click the words “Untitled history” on the new pane, and rename the new history.
  4. Add datasets by clicking and dragging them over from previous History panes.
  5. Click “Switch to” on the old history to return.

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For step-by-step instructions on how to link Gen3 and AnVIL to Terra, see this article. Once you're logged into your AnVIL-linked Terra account, you can launch your own instance of Galaxy through one of your workspaces.

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